Object of the predictModel class are used in various FLR classes to allow flexible modelling of the dynamics of different biological and technological processes.
Usage
# S4 method for class 'FLQuants,formula'
predictModel(object, model, params = FLPar())
# S4 method for class 'FLQuants,missing'
predictModel(object, params = FLPar())
# S4 method for class 'FLQuants,character'
predictModel(object, model, params = FLPar())
# S4 method for class 'FLQuants,function'
predictModel(object, model, params = FLPar())
# S4 method for class 'FLQuants,list'
predictModel(object, model, params = FLPar())
# S4 method for class 'missing,ANY'
predictModel(object, model, ...)Details
The dependency of life history processes, such as maturity and fecundity, to biological
and environmental factors, can be represented in objects of this class via a simple model
(represented by a formula) and the corresponding paramaters (FLPar) and inputs
(FLQuants).
Slots
- .Data
Inputs to the model not found in enclosing class (
FLQuants).- model
Model representation (
formula).- params
Model paramaters (
FLPar).
Validity
- VALIDITY
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You can inspect the class validity function by using
getValidity(getClassDef('predictModel'))
Accessors
All slots in the class have accessor and replacement methods defined that allow retrieving and substituting individual slots.
The values passed for replacement need to be of the class of that slot. A numeric vector can also be used when replacing FLQuant slots, and the vector will be used to substitute the values in the slot, but not its other attributes.
Constructor
A construction method exists for this class that can take named arguments for any of its slots. All slots are then created to match the requirements of the class validity.
Methods
Methods exist for various calculations based on values stored in the class:
- METHOD
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Examples
fec <- FLQuants(fec=FLQuant(rlnorm(10, 20, 5),
dimnames=list(year=2000:2009), units='1'))
predictModel(fec, model=~fec)
#> $ fec
#> An x of class "FLQuant"
#> , , unit = unique, season = all, area = unique
#>
#> year
#> quant 2000 2001 2002 2003 2004 2005 2006 2007
#> all 9.86e+11 2.00e+07 2.23e+11 1.77e+07 1.19e+08 1.77e+09 1.87e+10 4.36e+09
#> year
#> quant 2008 2009
#> all 1.23e+11 4.08e+06
#>
#> units: 1
#>
#> model:
#> ~fec
#> <environment: R_EmptyEnv>
#>
#> params:
#> An object of class "FLPar"
#> params
#>
#> NA
#> units: NA
predictModel(fec)
#> $ fec
#> An x of class "FLQuant"
#> , , unit = unique, season = all, area = unique
#>
#> year
#> quant 2000 2001 2002 2003 2004 2005 2006 2007
#> all 9.86e+11 2.00e+07 2.23e+11 1.77e+07 1.19e+08 1.77e+09 1.87e+10 4.36e+09
#> year
#> quant 2008 2009
#> all 1.23e+11 4.08e+06
#>
#> units: 1
#>
#> model:
#> ~NA
#> <environment: R_EmptyEnv>
#>
#> params:
#> An object of class "FLPar"
#> params
#>
#> NA
#> units: NA
predictModel(fec, model="bevholt")
#> $ fec
#> An x of class "FLQuant"
#> , , unit = unique, season = all, area = unique
#>
#> year
#> quant 2000 2001 2002 2003 2004 2005 2006 2007
#> all 9.86e+11 2.00e+07 2.23e+11 1.77e+07 1.19e+08 1.77e+09 1.87e+10 4.36e+09
#> year
#> quant 2008 2009
#> all 1.23e+11 4.08e+06
#>
#> units: 1
#>
#> model:
#> rec ~ a * ssb/(b + ssb)
#> <environment: R_EmptyEnv>
#>
#> params:
#> An object of class "FLPar"
#> params
#>
#> NA
#> units: NA
predictModel(fec, model=bevholt)
#> $ fec
#> An x of class "FLQuant"
#> , , unit = unique, season = all, area = unique
#>
#> year
#> quant 2000 2001 2002 2003 2004 2005 2006 2007
#> all 9.86e+11 2.00e+07 2.23e+11 1.77e+07 1.19e+08 1.77e+09 1.87e+10 4.36e+09
#> year
#> quant 2008 2009
#> all 1.23e+11 4.08e+06
#>
#> units: 1
#>
#> model:
#> rec ~ a * ssb/(b + ssb)
#> <environment: R_EmptyEnv>
#>
#> params:
#> An object of class "FLPar"
#> params
#>
#> NA
#> units: NA
predictModel(fec, model=bevholt())
#> $ fec
#> An x of class "FLQuant"
#> , , unit = unique, season = all, area = unique
#>
#> year
#> quant 2000 2001 2002 2003 2004 2005 2006 2007
#> all 9.86e+11 2.00e+07 2.23e+11 1.77e+07 1.19e+08 1.77e+09 1.87e+10 4.36e+09
#> year
#> quant 2008 2009
#> all 1.23e+11 4.08e+06
#>
#> units: 1
#>
#> model:
#> rec ~ a * ssb/(b + ssb)
#> <environment: R_EmptyEnv>
#>
#> params:
#> An object of class "FLPar"
#> params
#>
#> NA
#> units: NA
predictModel(model=rec~a*ssb, params=FLPar(a=1.234))
#> An object of class "FLQuants": EMPTY
#> model:
#> rec ~ a * ssb
#> <environment: R_EmptyEnv>
#>
#> params:
#> An object of class "FLPar"
#> params
#> a
#> 1.23
#> units: NA
predictModel(model=bevholt, params=FLPar(a=1.234))
#> An object of class "FLQuants": EMPTY
#> model:
#> rec ~ a * ssb/(b + ssb)
#> <environment: R_EmptyEnv>
#>
#> params:
#> An object of class "FLPar"
#> params
#> a
#> 1.23
#> units: NA
predictModel(model="bevholtss3", params=FLPar(a=1.234))
#> An object of class "FLQuants": EMPTY
#> model:
#> rec ~ (4 * s * R0 * ssb)/(v * (1 - s) + ssb * (5 * s - 1))
#> <environment: R_EmptyEnv>
#>
#> params:
#> An object of class "FLPar"
#> params
#> a
#> 1.23
#> units: NA